MultilayerPy (v1.0): a Python-based framework for building, running and optimising kinetic multi-layer models of aerosols and films

Abstract

Abstract. Kinetic multi-layer models of aerosols and films have become the state-of-the-art method of describing complex aerosol processes at the particle and film level. We present MultilayerPy: an open-source framework for building, running and optimising kinetic multi-layer models – namely the kinetic multi-layer model of aerosol surface and bulk chemistry (KM-SUB) and the kinetic multi-layer model of gas–particle interactions in aerosols and clouds (KM-GAP). The modular nature of this package allows the user to iterate through various reaction schemes, diffusion regimes and experimental conditions in a systematic way. In this way, models can be customised and the raw model code itself, produced in a readable way by MultilayerPy, is fully customisable. Optimisation to experimental data using local or global optimisation algorithms is included in the package along with the option to carry out statistical sampling and Bayesian inference of model parameters with a Markov chain Monte Carlo (MCMC) sampler (via the emcee Python package). MultilayerPy abstracts the model building process into separate building blocks, increasing the reproducibility of results and minimising human error. This paper describes the general functionality of MultilayerPy and demonstrates this with use cases based on the oleic- acid–ozone heterogeneous reaction system. The tutorials in the source code (written as Jupyter notebooks) and the documentation aim to encourage users to take advantage of this tool, which is intended to be developed in conjunction with the user base.

Aqueous Radical Initiated Oxidation of an Organic Monolayer at the Air–Water Interface as a Proxy for Thin Films on Atmospheric Aerosol Studied with Neutron Reflectometry

“…The characteristic time for transport of OH radicals to the interface is d 2 π 2 D , where d = 2.5 nm (the approximate size of the DSPC molecule at the air–water interface) and an estimate of the diffusion coefficient D = 2.8 × 10 –9 m 2 s –1 gives ∼0.2 ns. The characteristic reaction time is 1 k where k = 3.5 × 10 –4 s –1 taken from Table which gives a value with respect to reaction at the interface as ∼3000 s. A detailed mass-transfer calculation or multilayer diffusion model as described elsewhere , is thus not considered. The photolytic source of OH radicals from an enormous excess of nitrate anions was chosen to prevent a diffusive concentration profile from building up to the interface over the course of the long reaction time.…”

“…Characteristic time scales for diffusion and reaction can be estimated from simple formulas in Finlayson-Pitts and Pitts. 84 The characteristic time for transport of OH radicals to the interface is d 1 which gives a value with respect to reaction at the interface as ∼3000 s. A detailed mass-transfer calculation or multilayer diffusion model as described elsewhere 86,87 is thus not considered. The photolytic source of OH radicals from an enormous excess of nitrate anions was chosen to prevent a diffusive concentration profile from building up to the interface over the course of the long reaction time.…”

Molecular Self-Organization in Surfactant Atmospheric Aerosol Proxies

“…Recent developments in multilayer modeling include the incorporation of film growth mechanisms, the treatment of the lung epithelial lining fluid to derive health implications from these models, , an educational tool, and a move toward machine learning algorithms . We have recently published open-source software, MultilayerPy, which facilitates the creation and optimization of these models . MultilayerPy is free for anyone to use and has the potential to incorporate current and future multilayer models.…”

“…Kinetic multilayer modeling has helped us describe the impact of surfactant self-organization on processes at the aerosol and film levels. The recent development of MultilayerPy and methods to analyze the output of these models has increased the accessibility and interpretability of this kind of modeling. There is a need to efficiently link these computationally expensive models with large-scale atmospheric models that consider aerosols .…”

Acoustic levitation with polarising optical microscopy (AL-POM): water uptake in a nanostructured atmospheric aerosol proxy

“…We have devised a multi-layer approach to spatially and temporally resolve the uptake and diffusion of water through a self-assembled particle, incorporating changes in diffusivity caused by water content-dependent phase changes. This modelling approach is similar to those which resolve aerosol and surface and bulk chemistry [34][35][36][37][38] and ones which consider water uptake into viscous particles. 4,20,39 The multi-layer model is described in detail in the ESI †.…”